Contact Information

Name
Kota KASAHARA, Ph.D.
Position
Assistant Professor
Affiliation
Computational Structural Biology Lab., College of Life Sciences, Ritsumeikan University, Japan
Address
1-1-1, Noji-higashi, Kusatsu-shi, Shiga, 525-8577, Japan
E-mail
ktkshr <at> fc.ritsumeikan.ac.jp

Publication List

Articles

  • *: Corresponding author(s). / †: Joint first authors.
    1. †Ryosuke Iwai, *†Kota Kasahara, Takuya Takahashi,
      "Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant",
      2018, Biophysics and Physicobiology, 15:165-172, doi.org/10.2142/biophysico.15.0_165 URL
    2. †Naoki Ogasawara​, *†Kota Kasahara​​, Ryosuke Iwai, Takuya Takahashi,
      "Unfolding of α-helical 20-residue poly-glutamic acid analyzed by multiple runs of canonical molecular dynamics simulations",
      2018, PeerJ, 6:e4769, doi: 10.7717/peerj.4769 PubMed URL
    3. *Kota Kasahara, Shun Sakuraba, Ikuo Fukuda,
      "Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation",
      2018, The Journal of Physical Chemistry B, 122(9):2495-2503, doi: 10.1021/acs.jpcb.7b10830 PubMed URL
    4. Tomonori Hayami, Kota Kasahara, Haruki Nakamura, *Junichi Higo,
      "Molecular Dynamics Coupled with a Virtual System for Effective Conformational Sampling",
      2018, Journal of Computational Chemistry, 39(19):1291-1299, doi: 10.1002/jcc.25196 PubMed URL
    5. *†Kota Kasahara, *†Masaaki Shiina, Junichi Higo, Kazuhiro Ogata, Haruki Nakamura,
      "Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state.",
      2018, Nucleic Acids Research, 46(5):2243-2251, doi: 10.1093/nar/gkx1297 PubMed URL
    6. *Junichi Higo, Kota Kasahara, Haruki Nakamura,
      "Multi-dimensional virtual system introduced to enhance canonical sampling.",
      2017, The Journal of Chemical Physics, 147: 134102, doi: 10.1063/1.4986129 PubMed URL
    7. Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara,
      "OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation.",
      2017, Information Engineering Express, 3(2): 11-23, URL
    8. *Kota Kasahara, Masaaki Shiina, Ikuo Fukuda, Kazuhiro Ogata, Haruki Nakamura,
      "Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer.",
      2017, PLoS ONE, 12(2): e0172654, doi:10.1371/journal.pone.0172654 PubMed URL
    9. *Junichi Higo, Kota Kasahara, Bhaskar Dasgupta, Haruki Nakamura,
      "Enhancement of canonical sampling by virtual-state transitions",
      2017, The Journal of Chemical Physics, 146: 044104, doi: 10.1063/1.4974087 PubMed URL
    10. Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara,
      "An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL",
      2017, International Journal of Networked and Distributed Computing, 5(1):52-61, doi: 10.1109/ICIS.2016.7550743 URL
    11. *Kota Kasahara, Kengo Kinoshita,
      "IBiSA_tools: A Computational Toolkit for Ion-binding State Analysis in Molecular Dynamics Trajectories of Ion Channels ",
      2016, PLoS ONE, 11(12): e0167524, doi: 10.1371/journal.pone.0167524 PubMed URL
    12. *Kota Kasahara, Benson Ma, Kota Goto, Bhaskar Dasgupta, Junichi Higo, Ikuo Fukuda, Tadaaki Mashimo, Yutaka Akiyama, Haruki Nakamura,
      "myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme",
      2016, Biophysics and Physicobiology, 13:209-216, doi: 10.2142/biophysico.13.0_209 PubMed URL
    13. *Kota Kasahara, Kengo Kinoshita,
      "Landscape of protein-small ligand binding modes.",
      2016, Protein Science, 25(9):1659-71, doi: 10.1002/pro.2971 PubMed URL
    14. *Kota Kasahara, Neetha Mohan, Ikuo Fukuda, Haruki Nakamura,
      "mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories",
      2016, Bioinformatics, 32(16):2531-3, doi: 10.1093/bioinformatics/btw129 PubMed URL
    15. Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita,
      "Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction",
      2016, PLoS ONE, 11:e0150716, doi: 10.1371/journal.pone.0150716 PubMed URL
    16. *Junichi Higo, Bhaskar Dasgupta, Tadaaki Mashimo, Kota Kasahara, Yoshifumi Fukunishi, Haruki Nakamura,
      "Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.",
      2015, Journal of Computational Chemistry, 36(20):1489-501, doi: 10.1002/jcc.23948 PubMed URL
    17. *Kota Kasahara, Ikuo Fukuda, Haruki Nakamura,
      "A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer-DNA Complex.",
      2014, PLoS ONE, 9(11):e112419, doi: 10.1371/journal.pone.0112419 PubMed URL
    18. Bhaskar Dasgupta, Kota Kasahara, Narutoshi Kamiya, Haruki Nakamura, *Akira R Kinjo,
      "Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics",
      2014, PLoS ONE, 9:e91347, doi: 10.1371/journal.pone.0091347 PubMed URL
    19. Kota Kasahara, *Kengo Kinoshita,
      "GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes.",
      2014, BMC Bioinformatics, 15:12, doi: 10.1186/1471-2105-15-12 PubMed URL
    20. Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita,
      "Ion Concentration-Dependent Ion Conduction Mechanism of a Voltage-Sensitive Potassium Channel.",
      2013, PLoS ONE, 8:e56342, doi: 10.1371/journal.pone.0056342 PubMed URL
    21. Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita,
      "Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions.",
      2013, Journal of Chemical Information and Modeling, 53(1):241–248, doi: 10.1021/ci300377f PubMed URL
    22. *Takeshi Obayashi, Kozo Nishida, Kota Kasahara, Kengo Kinoshita,
      "ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.",
      2011, Plant and Cell Physiology, 52:213–219, doi: 10.1093/pcp/pcq203 PubMed URL
    23. *Kota Kasahara, Kengo Kinoshita, Toshihisa Takagi,
      "Ligand-binding site prediction of proteins based on known fragment-fragment interactions.",
      2010, Bioinformatics, 26(12):1493–1499, doi: 10.1093/bioinformatics/btq232 PubMed URL
    24. Kota Kasahara, Hideyuki Tsuboi, Michihisa Koyama, Akira Endou, Momoji Kubo, Calros Adriel Del Carpio, *Akira Miyamoto,
      "Tight-Binding Quantum Chemical Molecular Dynamics Study on First Proton Transfer Process of ORR Catalyzed by Cobalt-Porphyrin Complex.",
      2006, Electrochemical and Solid State Letters, 9:A490, doi: 10.1149/1.2336985 URL

    Reviews (Japanese)

    1. Kasahara K, Shirota M, Kinoshita K Molecular dynamics simulation, ion channel, dynamic structure, bioinformatics 2013 Seikagaku 85(8):656-662 PubMed

    Books (Japanese)

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    Software/Database

    Curriculum Vitae

    C.V.

    Jan 8th, 1983
    Hello, world.
    Apr,1st,1998−Mar,19th,2003
    Department of Material Engeneering, Nagaoka College, National Institute of Technology, Japan
    Apr,1st,2003−Mar,2005
    Department of Applied Chemistry, School of Engeneering, Tohoku University
    Undergraduate student
    (Supervisor: Prof. Akira Miyamoto)
    Apr,1st,2005−Mar,27th,2007
    Department of Applied Chemistry, Graduate School of Engeneering, Tohoku University
    Master course student
    (Supervisor: Prof. Akira Miyamoto)
    Apr,1st,2007−Sep,27th,2010
    Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo
    Ph.D. course student
    (Supervisor: Prof. Toshihisa Takagi)
    Apr,2008−Mar,2009
    Research Fellow of the Japan Society for the Promotion of Science (DC2)
    Oct,1st,2010−Dec,31st,2012
    Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University
    Postdoc.
    (PI: Prof. Kengo Kinoshita)
    Jan,1st,2013−Mar,31st,2016
    Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University
    Postdoc.
    (PI: Prof. Haruki Nakamura)
    Apr,1st,2016−Present
    Department of Bioinformatics, College of Life Sciences, Ritsumeikan University
    Assistant Professor.
    (PI: Prof. Takuya Takahashi)

    Affiliated Academic Organizations

    • Protein Science Society of Japan
    • Biophisical Society of Japan
    • Japanese Society for Bioinformatics